EWAS
As
DMP_As = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'As_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/As')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 23361
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 16750
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.933939
# Number of DMRs identified: 6
# rm(DMP_As); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
2
|
113992761
|
113993313
|
0.00e+00
|
552
|
0.00e+00
|
0.0000000
|
8
|
|
3
|
46759437
|
46759698
|
0.00e+00
|
261
|
0.00e+00
|
0.0000003
|
7
|
|
1
|
228395659
|
228396009
|
0.00e+00
|
350
|
0.00e+00
|
0.0000007
|
5
|
|
17
|
1395863
|
1396123
|
0.00e+00
|
260
|
0.00e+00
|
0.0000018
|
5
|
|
17
|
16593581
|
16593613
|
1.00e-07
|
32
|
1.00e-07
|
0.0007180
|
4
|
|
17
|
75315562
|
75315667
|
4.63e-05
|
105
|
4.63e-05
|
0.1596525
|
3
|
No adjustment for fish consumption
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/As/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/As/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/As/As_log2_manhattan_DMP_adj.png")

As, female
pDatAge7Metal_F = pDatAge7Metal[pDatAge7Metal$female_d == 1,]
pDatAge7Metal_F$race_child2 = as.factor(as.numeric(pDatAge7Metal_F$race_child2))
DMP_As_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'As_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/As_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 26064
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 15925
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9033443
# Number of DMRs identified: 4
rm(DMP_As_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
1
|
11561496
|
11561711
|
0.0e+00
|
215
|
0.0e+00
|
0.0000022
|
3
|
|
2
|
113992761
|
113993142
|
0.0e+00
|
381
|
0.0e+00
|
0.0000018
|
6
|
|
7
|
76027000
|
76027101
|
0.0e+00
|
101
|
0.0e+00
|
0.0000119
|
3
|
|
2
|
198651075
|
198651347
|
6.3e-06
|
272
|
6.3e-06
|
0.0090701
|
3
|
No adjustment for fish consumption
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/As_F/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/As_F/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/As_F/As_log2_manhattan_DMP_adj.png")

As, male
pDatAge7Metal_M = pDatAge7Metal[pDatAge7Metal$female_d == 0,]
pDatAge7Metal_M$race_child2 = as.factor(as.numeric(pDatAge7Metal_M$race_child2))
DMP_As_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'As_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/As_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 11497
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 14521
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8501198
# Number of DMRs identified: 3
# rm(DMP_As_M); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
47091977
|
47092178
|
0
|
201
|
0
|
1.2e-06
|
4
|
|
2
|
164204627
|
164205032
|
0
|
405
|
0
|
5.2e-06
|
5
|
|
5
|
6755149
|
6755439
|
0
|
290
|
0
|
2.1e-05
|
5
|
No adjustment for fish consumption
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/As_M/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/As_M/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/As_M/As_log2_manhattan_DMP_adj.png")

Ba
DMP_Ba = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Ba_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Ba')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 11801
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 11923
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.7860875
# Number of DMRs identified: 3
rm(DMP_Ba); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
6899084
|
6899577
|
0.000000
|
493
|
0.000000
|
0.0000000
|
10
|
|
16
|
1583809
|
1584118
|
0.000000
|
309
|
0.000000
|
0.0000083
|
6
|
|
6
|
32145551
|
32145654
|
0.000806
|
103
|
0.000806
|
0.9544043
|
5
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Ba/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Ba/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Ba/Ba_log2_manhattan_DMP_adj.png")

Ba, female
DMP_Ba_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Ba_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Ba_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 29651
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 23451
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.216079
rm(DMP_Ba_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
6899084
|
6899577
|
0.0000000
|
493
|
0.0000000
|
0.0000000
|
10
|
|
17
|
37123637
|
37123949
|
0.0000000
|
312
|
0.0000000
|
0.0000068
|
9
|
|
2
|
183943387
|
183943551
|
0.0000000
|
164
|
0.0000000
|
0.0000317
|
5
|
|
3
|
112359487
|
112359652
|
0.0000001
|
165
|
0.0000001
|
0.0001519
|
6
|
|
7
|
94285269
|
94285329
|
0.0000446
|
60
|
0.0000536
|
0.2543856
|
5
|
|
1
|
234367321
|
234367443
|
0.0002131
|
122
|
0.0002131
|
0.4978958
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Ba_F/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Ba_F/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Ba_F/Ba_log2_manhattan_DMP_adj.png")

Ba, male
DMP_Ba_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Ba_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Ba_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 25363
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 28150
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.261352
rm(DMP_Ba_M); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
16
|
1583809
|
1584118
|
0e+00
|
309
|
0e+00
|
0.00e+00
|
6
|
|
19
|
50194119
|
50194252
|
0e+00
|
133
|
0e+00
|
2.30e-06
|
5
|
|
6
|
29595001
|
29595335
|
1e-07
|
334
|
1e-07
|
9.07e-05
|
8
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Ba_M/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Ba_M/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Ba_M/Ba_log2_manhattan_DMP_adj.png")

Cd
DMP_Cd = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cd_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cd')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 9428
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 11922
# Adjusted, FDR<0.05: 1
# Adjusted, pBonf<0.05: 1
# Adjusted, lambda: 0.8236619
rm(DMP_Cd); gc()
FDR-significant DMPs
|
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
cg07044523
|
0.26 (0.17 ,0.34)
|
5.28
|
0
|
0.0017741
|
0.0018
|
chr1
|
153514376
|
S100A5
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
7
|
158045979
|
158046166
|
0.0000000
|
187
|
0.0000000
|
6.10e-06
|
3
|
|
5
|
23507449
|
23507656
|
0.0000000
|
207
|
0.0000000
|
1.43e-05
|
5
|
|
17
|
46685291
|
46685448
|
0.0000000
|
157
|
0.0000000
|
8.55e-05
|
5
|
|
7
|
27184158
|
27184188
|
0.0024888
|
30
|
0.0024888
|
1.00e+00
|
4
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cd/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cd/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cd/Cd_log2_manhattan_DMP_adj.png")

Cd, female
DMP_Cd_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cd_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cd_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 13276
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 13294
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8195885
# Number of DMRs identified: 7
# rm(DMP_Cd_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
6
|
32164926
|
32165321
|
0.0000000
|
395
|
0.0000000
|
0.0000000
|
7
|
|
17
|
46685291
|
46685448
|
0.0000000
|
157
|
0.0000000
|
0.0000003
|
5
|
|
6
|
1624385
|
1624442
|
0.0000000
|
57
|
0.0000001
|
0.0002031
|
2
|
|
5
|
23507449
|
23507656
|
0.0000001
|
207
|
0.0000001
|
0.0000961
|
5
|
|
6
|
88757301
|
88757392
|
0.0000001
|
91
|
0.0000001
|
0.0002665
|
5
|
|
11
|
73357094
|
73357276
|
0.0000030
|
182
|
0.0000035
|
0.0064276
|
6
|
|
5
|
132113754
|
132113860
|
0.0158178
|
106
|
0.0158178
|
1.0000000
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cd_F/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cd_F/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cd_F/Cd_log2_manhattan_DMP_adj.png")

Cd, male
DMP_Cd_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cd_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cd_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 16666
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 19823
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.072079
# Number of DMRs identified: 3
# rm(DMP_Cd_M); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
20
|
61446961
|
61447369
|
0.00e+00
|
408
|
0.00e+00
|
0.0000000
|
11
|
|
7
|
50518572
|
50518647
|
1.80e-06
|
75
|
2.70e-06
|
0.0093850
|
2
|
|
6
|
28446839
|
28447087
|
6.55e-05
|
248
|
6.55e-05
|
0.0989943
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cd_M/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cd_M/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cd_M/Cd_log2_manhattan_DMP_adj.png")

Cr
DMP_Cr = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cr_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cr')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 29723
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 23245
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.099732
# Number of identified DMR: 0
rm(DMP_Cr); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
No adjustment for fish consumption
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cr/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cr/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cr/Cr_log2_manhattan_DMP_adj.png")

Cr, female
DMP_Cr_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cr_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cr_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 26701
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 25616
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.219568
# Number of identified DMR: 0
rm(DMP_Cr_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
NA
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cr_F/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cr_F/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cr_F/Cr_log2_manhattan_DMP_adj.png")

Cr, male
DMP_Cr_M = run_wEWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cr_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cr_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 17887
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 12418
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8679592
# Number of DMRs identified: 1
rm(DMP_Cr_M); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
46685291
|
46685448
|
0
|
157
|
0
|
1.05e-05
|
5
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cr_M/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cr_M/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cr_M/Cr_log2_manhattan_DMP_adj.png")

Cs
DMP_Cs = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cs_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cs')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 16687
# Unadjusted, FDR<0.05: 4
# Unadjusted, pBonf<0.05: 2
# Adjusted, N = 333
# Adjusted, p<0.05: 13314
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8363101
# Number of DMRs identified: 4
rm(DMP_Cs); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
6
|
32847526
|
32847845
|
0.0000000
|
319
|
0.0000000
|
2.50e-06
|
16
|
|
6
|
33280051
|
33280228
|
0.0000000
|
177
|
0.0000001
|
6.02e-05
|
6
|
|
13
|
47472137
|
47472429
|
0.0000000
|
292
|
0.0000001
|
5.48e-05
|
10
|
|
20
|
57427729
|
57427762
|
0.0124658
|
33
|
0.0124658
|
1.00e+00
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cs/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cs/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cs/Cs_log2_manhattan_DMP_adj.png")

Cs, female
DMP_Cs_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cs_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cs_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 25871
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 15950
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9510468
# Number of DMRs identified: 4
rm(DMP_Cs_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
1
|
200272111
|
200272215
|
0
|
104
|
0
|
5.70e-06
|
3
|
|
6
|
29648378
|
29648628
|
0
|
250
|
0
|
2.89e-05
|
8
|
|
20
|
3145355
|
3145597
|
0
|
242
|
0
|
3.76e-05
|
3
|
|
5
|
78985424
|
78985592
|
0
|
168
|
0
|
9.92e-05
|
9
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cs_F/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cs_F/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cs_F/Cs_log2_manhattan_DMP_adj.png")

Cs, male
DMP_Cs_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cs_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cs_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 15896
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 14066
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8664272
# rm(DMP_Cs_M); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
20
|
57427442
|
57427973
|
0
|
531
|
0
|
0
|
17
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cs_M/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cs_M/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cs_M/Cs_log2_manhattan_DMP_adj.png")

Cu
DMP_Cu = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cu_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cu')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 10199
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 19919
# Adjusted, FDR<0.05: 29
# Adjusted, pBonf<0.05: 7
# Adjusted, lambda: 1.081857
# Number of DMRs identified: 18
# rm(DMP_Cu); gc()
FDR-significant DMPs
|
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
cg00082497
|
-0.25 (-0.36 ,-0.15)
|
-5.32
|
2.6e-06
|
0.0361295
|
1.0000
|
chr1
|
32802133
|
MARCKSL1
|
|
cg00116766
|
0.42 (0.28 ,0.56)
|
2.04
|
0.0e+00
|
0.0010722
|
0.0018
|
chr16
|
9857614
|
GRIN2A;GRIN2A;GRIN2A
|
|
cg00908120
|
0.51 (0.33 ,0.7)
|
6.26
|
1.0e-07
|
0.0063015
|
0.0567
|
chr16
|
72872925
|
ZFHX3;ZFHX3
|
|
cg02155957
|
0.38 (0.23 ,0.52)
|
3.25
|
6.0e-07
|
0.0142130
|
0.2558
|
chr1
|
46930731
|
|
|
cg04015129
|
0.7 (0.44 ,0.96)
|
4.28
|
3.0e-07
|
0.0085878
|
0.1031
|
chr10
|
1058036
|
GTPBP4
|
|
cg04692924
|
-0.42 (-0.59 ,-0.26)
|
-6.61
|
1.0e-06
|
0.0183556
|
0.3855
|
chr1
|
161720042
|
DUSP12
|
|
cg05051957
|
-0.45 (-0.63 ,-0.28)
|
-5.60
|
4.0e-07
|
0.0108039
|
0.1621
|
chr8
|
141522459
|
CHRAC1;CHRAC1
|
|
cg05955013
|
-0.39 (-0.54 ,-0.24)
|
-6.28
|
5.0e-07
|
0.0111376
|
0.1782
|
chr17
|
45056646
|
RPRML
|
|
cg06723863
|
-0.26 (-0.36 ,-0.15)
|
-5.98
|
1.8e-06
|
0.0289638
|
0.6994
|
chr16
|
68270129
|
ESRP2;ESRP2
|
|
cg07380021
|
-0.5 (-0.69 ,-0.32)
|
-5.42
|
1.0e-07
|
0.0063015
|
0.0541
|
chr1
|
206755252
|
RASSF5;RASSF5;RASSF5
|
|
cg07831553
|
0.6 (0.36 ,0.85)
|
3.37
|
2.7e-06
|
0.0361295
|
1.0000
|
chr19
|
48796974
|
|
|
cg08370347
|
0.51 (0.3 ,0.71)
|
3.91
|
1.9e-06
|
0.0289638
|
0.7331
|
chr5
|
171571793
|
STK10
|
|
cg10145926
|
0.61 (0.38 ,0.83)
|
5.31
|
2.0e-07
|
0.0073929
|
0.0813
|
chr14
|
95875792
|
C14orf139
|
|
cg10653573
|
0.82 (0.49 ,1.15)
|
5.43
|
1.4e-06
|
0.0244817
|
0.5386
|
chr8
|
141347297
|
TRAPPC9;TRAPPC9
|
|
cg10923018
|
0.24 (0.16 ,0.32)
|
2.75
|
0.0e+00
|
0.0028603
|
0.0145
|
chr6
|
31743769
|
C6orf27
|
|
cg11608893
|
0.61 (0.36 ,0.85)
|
6.05
|
1.9e-06
|
0.0289638
|
0.7596
|
chr6
|
32059542
|
TNXB
|
|
cg12067421
|
-0.47 (-0.62 ,-0.31)
|
2.01
|
0.0e+00
|
0.0010722
|
0.0032
|
chr1
|
203246482
|
|
|
cg13434714
|
-0.42 (-0.58 ,-0.26)
|
-5.77
|
8.0e-07
|
0.0168736
|
0.3206
|
chr12
|
6936787
|
LEPREL2
|
|
cg15790767
|
1.04 (0.66 ,1.42)
|
3.84
|
1.0e-07
|
0.0063015
|
0.0455
|
chr6
|
13431216
|
GFOD1
|
|
cg17143270
|
0.83 (0.52 ,1.14)
|
5.74
|
3.0e-07
|
0.0093778
|
0.1313
|
chr1
|
91532819
|
|
|
cg18299835
|
-0.23 (-0.33 ,-0.14)
|
-4.13
|
2.0e-06
|
0.0289638
|
0.7820
|
chr19
|
13207445
|
NFIX
|
|
cg18714712
|
-0.54 (-0.72 ,-0.36)
|
-5.97
|
0.0e+00
|
0.0010722
|
0.0030
|
chr19
|
49866917
|
DKKL1;TEAD2
|
|
cg19532212
|
0.49 (0.3 ,0.67)
|
4.46
|
3.0e-07
|
0.0087176
|
0.1133
|
chr17
|
56769430
|
TEX14;RAD51C;TEX14;RAD51C
|
|
cg19842134
|
-0.29 (-0.4 ,-0.17)
|
-3.53
|
9.0e-07
|
0.0170970
|
0.3419
|
chr12
|
54070591
|
ATP5G2;ATP5G2
|
|
cg20365618
|
-0.24 (-0.34 ,-0.15)
|
0.42
|
1.4e-06
|
0.0245000
|
0.5635
|
chr10
|
121578384
|
INPP5F;INPP5F
|
|
cg23477849
|
0.28 (0.19 ,0.38)
|
4.88
|
0.0e+00
|
0.0023982
|
0.0096
|
chr19
|
5698492
|
LONP1
|
|
cg25954729
|
-0.22 (-0.3 ,-0.14)
|
-6.34
|
2.0e-07
|
0.0064642
|
0.0646
|
chr11
|
66610784
|
RCE1;C11orf80;RCE1
|
|
cg26708724
|
0.66 (0.41 ,0.91)
|
6.73
|
5.0e-07
|
0.0123375
|
0.2097
|
chr4
|
187509785
|
FAT1
|
|
cg27565067
|
0.48 (0.31 ,0.65)
|
6.20
|
0.0e+00
|
0.0028603
|
0.0172
|
chr17
|
149484
|
RPH3AL
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
22
|
45704901
|
45705265
|
0.0e+00
|
364
|
0.0e+00
|
0.0000000
|
7
|
|
20
|
35169538
|
35169886
|
0.0e+00
|
348
|
0.0e+00
|
0.0000000
|
6
|
|
16
|
66304366
|
66304585
|
0.0e+00
|
219
|
0.0e+00
|
0.0000001
|
3
|
|
10
|
121578136
|
121578639
|
0.0e+00
|
503
|
0.0e+00
|
0.0000001
|
4
|
|
12
|
54070516
|
54070610
|
0.0e+00
|
94
|
0.0e+00
|
0.0000007
|
5
|
|
16
|
8806530
|
8806756
|
0.0e+00
|
226
|
0.0e+00
|
0.0000004
|
7
|
|
17
|
149483
|
149488
|
0.0e+00
|
5
|
0.0e+00
|
0.0001511
|
2
|
|
6
|
1604012
|
1604212
|
0.0e+00
|
200
|
0.0e+00
|
0.0000158
|
5
|
|
20
|
3052114
|
3052483
|
0.0e+00
|
369
|
0.0e+00
|
0.0000229
|
9
|
|
17
|
1395863
|
1396123
|
0.0e+00
|
260
|
0.0e+00
|
0.0000413
|
5
|
|
19
|
55660590
|
55660625
|
0.0e+00
|
35
|
0.0e+00
|
0.0003111
|
4
|
|
2
|
130345204
|
130345405
|
1.0e-07
|
201
|
1.0e-07
|
0.0001057
|
3
|
|
15
|
100048370
|
100048500
|
1.0e-07
|
130
|
1.0e-07
|
0.0001709
|
3
|
|
17
|
47091977
|
47092178
|
1.0e-07
|
201
|
1.0e-07
|
0.0001289
|
4
|
|
19
|
50194119
|
50194252
|
1.0e-07
|
133
|
1.0e-07
|
0.0002880
|
5
|
|
13
|
100310161
|
100310405
|
1.0e-07
|
244
|
1.0e-07
|
0.0001625
|
4
|
|
11
|
19736149
|
19736333
|
1.0e-07
|
184
|
1.0e-07
|
0.0002511
|
5
|
|
1
|
207082827
|
207082900
|
1.3e-06
|
73
|
1.3e-06
|
0.0067921
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cu/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cu/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cu/Cu_log2_manhattan_DMP_adj.png")

Cu, female
DMP_Cu_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cu_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cu_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 19233
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 16219
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9599566
# Number of DMRs identified: 11
# chr start end p length fdr sidak nprobe
# 1 5 191295 191806 2.084698e-12 511 2.293168e-11 1.609231e-09 9
# 2 6 32063990 32064810 4.914157e-12 820 2.702787e-11 2.363960e-09 30
# 3 15 81426346 81426610 1.166735e-10 264 4.278029e-10 1.743297e-07 7
# 4 11 73357094 73357396 3.201810e-08 302 8.804977e-08 4.181985e-05 7
# 5 2 74875226 74875536 5.410336e-08 310 1.190274e-07 6.884154e-05 7
# 6 21 37442288 37442476 1.402076e-07 188 2.309027e-07 2.941391e-04 3
# 7 1 120174148 120174361 1.507576e-07 213 2.309027e-07 2.791527e-04 2
# 8 17 1395863 1396123 1.679292e-07 260 2.309027e-07 2.547420e-04 5
# 9 8 95962351 95962383 2.534889e-06 32 3.098197e-06 3.076414e-02 4
# 10 6 31734191 31734401 3.970020e-05 210 4.367022e-05 7.186081e-02 6
# 11 19 23941312 23941438 1.175697e-04 126 1.175697e-04 3.079446e-01 3
# rm(DMP_Cu_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
5
|
191295
|
191806
|
0.0000000
|
511
|
0.0000000
|
0.0000000
|
9
|
|
6
|
32063990
|
32064810
|
0.0000000
|
820
|
0.0000000
|
0.0000000
|
30
|
|
15
|
81426346
|
81426610
|
0.0000000
|
264
|
0.0000000
|
0.0000002
|
7
|
|
11
|
73357094
|
73357396
|
0.0000000
|
302
|
0.0000001
|
0.0000418
|
7
|
|
2
|
74875226
|
74875536
|
0.0000001
|
310
|
0.0000001
|
0.0000688
|
7
|
|
21
|
37442288
|
37442476
|
0.0000001
|
188
|
0.0000002
|
0.0002941
|
3
|
|
1
|
120174148
|
120174361
|
0.0000002
|
213
|
0.0000002
|
0.0002792
|
2
|
|
17
|
1395863
|
1396123
|
0.0000002
|
260
|
0.0000002
|
0.0002547
|
5
|
|
8
|
95962351
|
95962383
|
0.0000025
|
32
|
0.0000031
|
0.0307641
|
4
|
|
6
|
31734191
|
31734401
|
0.0000397
|
210
|
0.0000437
|
0.0718608
|
6
|
|
19
|
23941312
|
23941438
|
0.0001176
|
126
|
0.0001176
|
0.3079446
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cu_F/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cu_F/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cu_F/Cu_log2_manhattan_DMP_adj.png")

Cu, male
DMP_Cu_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cu_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cu_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 8255
# Unadjusted, FDR<0.05: 32
# Unadjusted, pBonf<0.05: 5
# Adjusted, N = 175
# Adjusted, p<0.05: 12165
# Adjusted, FDR<0.05: 46
# Adjusted, pBonf<0.05: 13
# Adjusted, lambda: 0.7385324
# Number of DMRs identified: 13
# rm(DMP_Cu_M); gc()
FDR-significant DMPs
|
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
cg00908120
|
0.7 (0.45 ,0.95)
|
6.29
|
1.0e-07
|
0.0036055
|
0.0505
|
chr16
|
72872925
|
ZFHX3;ZFHX3
|
|
cg01007589
|
0.93 (0.61 ,1.26)
|
4.79
|
1.0e-07
|
0.0024477
|
0.0282
|
chr19
|
49894178
|
CCDC155
|
|
cg01063965
|
-0.27 (-0.38 ,-0.17)
|
-6.44
|
3.0e-07
|
0.0080101
|
0.1323
|
chr11
|
695461
|
TMEM80;TMEM80;DEAF1;DEAF1
|
|
cg01447660
|
0.38 (0.22 ,0.53)
|
-0.92
|
4.3e-06
|
0.0399576
|
1.0000
|
chr2
|
69152678
|
|
|
cg01485439
|
0.5 (0.31 ,0.69)
|
3.65
|
8.0e-07
|
0.0143550
|
0.3169
|
chr11
|
67225937
|
CABP4
|
|
cg02155957
|
0.48 (0.29 ,0.67)
|
3.22
|
1.6e-06
|
0.0203703
|
0.6165
|
chr1
|
46930731
|
|
|
cg02196294
|
-0.26 (-0.37 ,-0.15)
|
-5.41
|
5.0e-06
|
0.0450418
|
1.0000
|
chr6
|
39197260
|
KCNK5
|
|
cg02490920
|
0.37 (0.23 ,0.51)
|
1.34
|
4.0e-07
|
0.0080101
|
0.1437
|
chr3
|
50304406
|
SEMA3B;SEMA3B
|
|
cg02968175
|
0.31 (0.19 ,0.42)
|
5.76
|
4.0e-07
|
0.0080101
|
0.1386
|
chr16
|
4690020
|
MGRN1;MGRN1;MGRN1;MGRN1
|
|
cg03717239
|
0.3 (0.18 ,0.42)
|
0.51
|
2.6e-06
|
0.0277414
|
1.0000
|
chr8
|
145574318
|
|
|
cg04015129
|
0.84 (0.56 ,1.13)
|
4.27
|
0.0e+00
|
0.0010730
|
0.0097
|
chr10
|
1058036
|
GTPBP4
|
|
cg04406071
|
-0.3 (-0.41 ,-0.19)
|
-6.07
|
4.0e-07
|
0.0080101
|
0.1442
|
chr17
|
59489784
|
C17orf82
|
|
cg04692924
|
-0.6 (-0.83 ,-0.36)
|
-6.58
|
1.1e-06
|
0.0160189
|
0.4165
|
chr1
|
161720042
|
DUSP12
|
|
cg05051957
|
-0.61 (-0.85 ,-0.37)
|
-5.61
|
1.7e-06
|
0.0203703
|
0.6518
|
chr8
|
141522459
|
CHRAC1;CHRAC1
|
|
cg05955013
|
-0.48 (-0.67 ,-0.29)
|
-6.30
|
2.1e-06
|
0.0238012
|
0.8092
|
chr17
|
45056646
|
RPRML
|
|
cg07380021
|
-0.68 (-0.9 ,-0.46)
|
-5.43
|
0.0e+00
|
0.0008408
|
0.0025
|
chr1
|
206755252
|
RASSF5;RASSF5;RASSF5
|
|
cg08329655
|
-0.43 (-0.6 ,-0.26)
|
-5.88
|
1.2e-06
|
0.0169324
|
0.4680
|
chr11
|
7534677
|
PPFIBP2
|
|
cg08459368
|
0.59 (0.36 ,0.82)
|
2.70
|
1.0e-06
|
0.0160189
|
0.4117
|
chr11
|
61974948
|
SCGB2A1
|
|
cg08760128
|
0.31 (0.19 ,0.43)
|
6.73
|
8.0e-07
|
0.0143550
|
0.3302
|
chr16
|
4723507
|
MGRN1;MGRN1;MGRN1;MGRN1
|
|
cg10053073
|
-0.21 (-0.31 ,-0.12)
|
0.54
|
5.5e-06
|
0.0484367
|
1.0000
|
chr17
|
73623182
|
RECQL5
|
|
cg10266648
|
1.04 (0.68 ,1.41)
|
5.98
|
1.0e-07
|
0.0024477
|
0.0318
|
chr2
|
106560529
|
|
|
cg10923018
|
0.35 (0.24 ,0.47)
|
2.73
|
0.0e+00
|
0.0006035
|
0.0012
|
chr6
|
31743769
|
C6orf27
|
|
cg11608893
|
0.95 (0.64 ,1.26)
|
6.08
|
0.0e+00
|
0.0008871
|
0.0040
|
chr6
|
32059542
|
TNXB
|
|
cg12243007
|
0.45 (0.26 ,0.64)
|
-0.77
|
4.5e-06
|
0.0409168
|
1.0000
|
chr17
|
184018
|
RPH3AL
|
|
cg13434714
|
-0.67 (-0.86 ,-0.47)
|
-5.78
|
0.0e+00
|
0.0001002
|
0.0001
|
chr12
|
6936787
|
LEPREL2
|
|
cg13989834
|
0.54 (0.33 ,0.75)
|
3.14
|
1.3e-06
|
0.0181143
|
0.5253
|
chr9
|
134400392
|
UCK1;UCK1
|
|
cg15389183
|
-0.22 (-0.31 ,-0.13)
|
-6.19
|
2.3e-06
|
0.0264805
|
0.9268
|
chr14
|
102829482
|
TECPR2;CINP
|
|
cg15790767
|
1.18 (0.69 ,1.66)
|
3.86
|
3.8e-06
|
0.0370497
|
1.0000
|
chr6
|
13431216
|
GFOD1
|
|
cg16068812
|
-1.01 (-1.42 ,-0.61)
|
-4.27
|
2.0e-06
|
0.0238012
|
0.8051
|
chr21
|
44528396
|
U2AF1;U2AF1;U2AF1
|
|
cg16496814
|
0.28 (0.17 ,0.39)
|
5.22
|
1.2e-06
|
0.0169324
|
0.4741
|
chr11
|
9778721
|
|
|
cg16656826
|
0.33 (0.2 ,0.45)
|
0.14
|
6.0e-07
|
0.0126948
|
0.2539
|
chr5
|
159343871
|
ADRA1B;ADRA1B
|
|
cg18670846
|
0.73 (0.43 ,1.03)
|
-2.30
|
3.9e-06
|
0.0378865
|
1.0000
|
chr2
|
68917482
|
|
|
cg18714712
|
-0.73 (-0.97 ,-0.48)
|
-5.95
|
0.0e+00
|
0.0010211
|
0.0082
|
chr19
|
49866917
|
DKKL1;TEAD2
|
|
cg19005275
|
0.68 (0.45 ,0.92)
|
4.29
|
0.0e+00
|
0.0016338
|
0.0163
|
chr12
|
113588263
|
CCDC42B
|
|
cg19532212
|
0.7 (0.44 ,0.96)
|
4.42
|
4.0e-07
|
0.0080757
|
0.1534
|
chr17
|
56769430
|
TEX14;RAD51C;TEX14;RAD51C
|
|
cg20365618
|
-0.35 (-0.46 ,-0.23)
|
0.40
|
0.0e+00
|
0.0010211
|
0.0081
|
chr10
|
121578384
|
INPP5F;INPP5F
|
|
cg21373263
|
0.79 (0.49 ,1.1)
|
3.29
|
7.0e-07
|
0.0137845
|
0.2895
|
chr10
|
126751982
|
CTBP2;CTBP2
|
|
cg21864868
|
0.66 (0.4 ,0.92)
|
4.22
|
9.0e-07
|
0.0153134
|
0.3675
|
chr17
|
46673002
|
LOC404266;LOC404266;LOC404266;LOC404266;LOC404266
|
|
cg22240394
|
1.04 (0.62 ,1.46)
|
6.82
|
2.6e-06
|
0.0277414
|
1.0000
|
chr3
|
186211630
|
|
|
cg22286640
|
-0.78 (-1.1 ,-0.46)
|
-4.65
|
3.6e-06
|
0.0363886
|
1.0000
|
chr8
|
67026828
|
|
|
cg23312431
|
0.34 (0.2 ,0.47)
|
-0.37
|
1.6e-06
|
0.0203703
|
0.6357
|
chr21
|
45773997
|
TRPM2
|
|
cg23477849
|
0.39 (0.25 ,0.52)
|
4.90
|
1.0e-07
|
0.0024477
|
0.0312
|
chr19
|
5698492
|
LONP1
|
|
cg24543538
|
0.83 (0.49 ,1.16)
|
3.22
|
2.7e-06
|
0.0281802
|
1.0000
|
chr2
|
241569846
|
GPR35
|
|
cg25954729
|
-0.31 (-0.41 ,-0.2)
|
-6.37
|
0.0e+00
|
0.0010211
|
0.0064
|
chr11
|
66610784
|
RCE1;C11orf80;RCE1
|
|
cg26708724
|
0.97 (0.65 ,1.28)
|
6.72
|
0.0e+00
|
0.0008871
|
0.0044
|
chr4
|
187509785
|
FAT1
|
|
cg27503275
|
0.43 (0.25 ,0.61)
|
4.12
|
5.7e-06
|
0.0487795
|
1.0000
|
chr6
|
3880016
|
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
10
|
121578136
|
121578846
|
0.0000000
|
710
|
0.0000000
|
0.0000000
|
5
|
|
22
|
45704901
|
45705265
|
0.0000000
|
364
|
0.0000000
|
0.0000000
|
7
|
|
21
|
45773781
|
45773997
|
0.0000000
|
216
|
0.0000000
|
0.0000008
|
2
|
|
4
|
24796918
|
24797176
|
0.0000000
|
258
|
0.0000000
|
0.0000028
|
6
|
|
19
|
50194119
|
50194252
|
0.0000000
|
133
|
0.0000000
|
0.0000115
|
5
|
|
17
|
70723226
|
70723386
|
0.0000000
|
160
|
0.0000000
|
0.0000390
|
2
|
|
20
|
35169593
|
35169886
|
0.0000000
|
293
|
0.0000000
|
0.0000228
|
5
|
|
3
|
16216093
|
16216215
|
0.0000000
|
122
|
0.0000001
|
0.0001340
|
4
|
|
14
|
78447480
|
78447640
|
0.0000000
|
160
|
0.0000001
|
0.0001027
|
3
|
|
17
|
78549323
|
78549371
|
0.0000001
|
48
|
0.0000001
|
0.0005317
|
3
|
|
17
|
149483
|
149488
|
0.0000001
|
5
|
0.0000001
|
0.0062718
|
2
|
|
12
|
54070516
|
54070591
|
0.0000102
|
75
|
0.0000110
|
0.0521028
|
4
|
|
16
|
8806752
|
8806756
|
0.0028704
|
4
|
0.0028704
|
1.0000000
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cu_M/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cu_M/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Cu_M/Cu_log2_manhattan_DMP_adj.png")

Hg
DMP_Hg = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Hg_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Hg')
# Unadjusted, N = 326
# Unadjusted, p<0.05: 37293
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 326
# Adjusted, p<0.05: 28324
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.24761
# Number of DMRs identified: 4
# rm(DMP_Hg); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
46681110
|
46681401
|
0.0000000
|
291
|
0.0000000
|
0.0000012
|
6
|
|
6
|
31846768
|
31847009
|
0.0000000
|
241
|
0.0000000
|
0.0000145
|
9
|
|
10
|
131843516
|
131843725
|
0.0000023
|
209
|
0.0000031
|
0.0043852
|
3
|
|
3
|
42977952
|
42978026
|
0.0004605
|
74
|
0.0004605
|
0.9141599
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Hg/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Hg/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Hg/Hg_log2_manhattan_DMP_adj.png")

Hg, female
DMP_Hg_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Hg_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Hg_F')
# Unadjusted, N = 154
# Unadjusted, p<0.05: 35686
# Unadjusted, FDR<0.05: 156
# Unadjusted, pBonf<0.05: 1
# Adjusted, N = 154
# Adjusted, p<0.05: 15125
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8835584
# Number of DMRs identified: 3
# rm(DMP_Hg_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
12
|
47219625
|
47220092
|
0
|
467
|
0
|
0.00e+00
|
12
|
|
4
|
165877874
|
165878136
|
0
|
262
|
0
|
3.10e-06
|
6
|
|
7
|
27143234
|
27143478
|
0
|
244
|
0
|
4.58e-05
|
7
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Hg_F/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Hg_F/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Hg_F/Hg_log2_manhattan_DMP_adj.png")

Hg, male
DMP_Hg_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Hg_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Hg_M')
# Unadjusted, N = 172
# Unadjusted, p<0.05: 22412
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 172
# Adjusted, p<0.05: 26536
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.269744
# Number of DMRs identified: 10
# rm(DMP_Hg_M); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
6
|
31846768
|
31847009
|
0.0000000
|
241
|
0.0000000
|
0.0000000
|
9
|
|
11
|
18477152
|
18477680
|
0.0000000
|
528
|
0.0000000
|
0.0000000
|
8
|
|
11
|
18433499
|
18433887
|
0.0000000
|
388
|
0.0000000
|
0.0000000
|
5
|
|
5
|
502290
|
502571
|
0.0000000
|
281
|
0.0000000
|
0.0000009
|
3
|
|
6
|
33282735
|
33283162
|
0.0000000
|
427
|
0.0000000
|
0.0000020
|
20
|
|
14
|
104690039
|
104690244
|
0.0000000
|
205
|
0.0000000
|
0.0000089
|
5
|
|
1
|
147737015
|
147737207
|
0.0000001
|
192
|
0.0000002
|
0.0003078
|
4
|
|
1
|
2345151
|
2345410
|
0.0000002
|
259
|
0.0000002
|
0.0002524
|
8
|
|
1
|
117317981
|
117318133
|
0.0009779
|
152
|
0.0010866
|
0.9210590
|
2
|
|
11
|
368613
|
368683
|
0.0015854
|
70
|
0.0015854
|
0.9998691
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Hg_M/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Hg_M/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Hg_M/Hg_log2_manhattan_DMP_adj.png")

Mg
DMP_Mg = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Mg_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mg')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 18232
# Unadjusted, FDR<0.05: 1
# Unadjusted, pBonf<0.05: 1
# Adjusted, N = 333
# Adjusted, p<0.05: 15760
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8766869
# Number of DMRs identified: 4
# rm(DMP_Mg); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
20
|
3051953
|
3052483
|
0.0e+00
|
530
|
0.0e+00
|
0.0000000
|
10
|
|
2
|
240196768
|
240196996
|
0.0e+00
|
228
|
1.0e-07
|
0.0000647
|
3
|
|
6
|
31543539
|
31543686
|
0.0e+00
|
147
|
1.0e-07
|
0.0001052
|
8
|
|
11
|
368564
|
368712
|
1.6e-06
|
148
|
1.6e-06
|
0.0043050
|
7
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mg/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mg/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mg/Mg_log2_manhattan_DMP_adj.png")

Mg, female
DMP_Mg_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Mg_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mg_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 33977
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 20218
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.061758
# Number of DMRs identified: 1
# rm(DMP_Mg_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
6
|
10884093
|
10884140
|
0.0002934
|
47
|
0.0002934
|
0.9147992
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mg_F/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mg_F/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mg_F/Mg_log2_manhattan_DMP_adj.png")

Mg, male
DMP_Mg_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Mg_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mg_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 9395
# Unadjusted, FDR<0.05: 7
# Unadjusted, pBonf<0.05: 5
# Adjusted, N = 175
# Adjusted, p<0.05: 12911
# Adjusted, FDR<0.05: 3
# Adjusted, pBonf<0.05: 3
# Adjusted, lambda: 0.7788244
# Number of DMRs identified: 3
# rm(DMP_Mg_M); gc()
FDR-significant DMPs
|
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
cg13434714
|
-0.59 (-0.78 ,-0.41)
|
-5.78
|
0e+00
|
0.0016685
|
0.0017
|
chr12
|
6936787
|
LEPREL2
|
|
cg18670846
|
0.83 (0.55 ,1.1)
|
-2.30
|
0e+00
|
0.0035334
|
0.0071
|
chr2
|
68917482
|
|
|
cg26708724
|
0.88 (0.57 ,1.18)
|
6.72
|
1e-07
|
0.0073831
|
0.0221
|
chr4
|
187509785
|
FAT1
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
2
|
152830504
|
152830665
|
0
|
161
|
0
|
4.49e-05
|
5
|
|
17
|
37123668
|
37123949
|
0
|
281
|
0
|
4.39e-05
|
8
|
|
5
|
23507449
|
23507656
|
0
|
207
|
0
|
9.40e-05
|
5
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mg_M/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mg_M/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mg_M/Mg_log2_manhattan_DMP_adj.png")

Mn
DMP_Mn = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Mn_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mn')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 27983
# Unadjusted, FDR<0.05: 6
# Unadjusted, pBonf<0.05: 1
# Adjusted, N = 333
# Adjusted, p<0.05: 39522
# Adjusted, FDR<0.05: 13
# Adjusted, pBonf<0.05: 3
# Adjusted, lambda: 1.362045
# Number of DMRs identified: 8
# rm(DMP_Mn); gc()
FDR-significant DMPs
|
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
cg00808511
|
0.18 (0.11 ,0.25)
|
2.86
|
1.6e-06
|
0.0495452
|
0.6441
|
chr16
|
52495237
|
TOX3;TOX3
|
|
cg03716590
|
0.18 (0.11 ,0.25)
|
5.09
|
8.0e-07
|
0.0324264
|
0.3243
|
chr7
|
95435309
|
DYNC1I1;DYNC1I1;DYNC1I1
|
|
cg05613017
|
0.2 (0.12 ,0.28)
|
5.33
|
5.0e-07
|
0.0226928
|
0.2042
|
chr12
|
65589446
|
LEMD3;LEMD3
|
|
cg09856068
|
-0.11 (-0.16 ,-0.07)
|
-4.37
|
5.0e-07
|
0.0226928
|
0.1878
|
chr5
|
170878246
|
FGF18
|
|
cg11063328
|
-0.16 (-0.22 ,-0.1)
|
-6.02
|
4.0e-07
|
0.0226928
|
0.1593
|
chr11
|
18343203
|
GTF2H1;HPS5;HPS5;HPS5;GTF2H1
|
|
cg13834844
|
-0.1 (-0.14 ,-0.06)
|
-5.14
|
1.0e-07
|
0.0140080
|
0.0560
|
chr10
|
102415320
|
|
|
cg14252211
|
0.19 (0.13 ,0.26)
|
5.85
|
0.0e+00
|
0.0030032
|
0.0060
|
chr1
|
25919394
|
|
|
cg19407717
|
0.31 (0.22 ,0.4)
|
4.03
|
0.0e+00
|
0.0000228
|
0.0000
|
chr2
|
1544120
|
TPO;TPO;TPO;TPO
|
|
cg19425870
|
-0.15 (-0.21 ,-0.09)
|
-6.46
|
1.0e-06
|
0.0366926
|
0.4036
|
chr11
|
3876808
|
STIM1
|
|
cg22586726
|
0.27 (0.16 ,0.38)
|
-0.97
|
1.5e-06
|
0.0495452
|
0.6014
|
chr10
|
134150542
|
LRRC27;LRRC27;LRRC27;LRRC27;LRRC27
|
|
cg24196240
|
0.33 (0.21 ,0.45)
|
5.25
|
1.0e-07
|
0.0119610
|
0.0359
|
chr21
|
36096009
|
NCRNA00160
|
|
cg25101184
|
0.25 (0.15 ,0.34)
|
3.38
|
4.0e-07
|
0.0226928
|
0.1753
|
chr14
|
56231604
|
RPL13AP3
|
|
cg27095984
|
-0.19 (-0.26 ,-0.12)
|
5.27
|
3.0e-07
|
0.0224715
|
0.1124
|
chr13
|
21652115
|
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
10
|
134150488
|
134150760
|
0.0000000
|
272
|
0.0000000
|
0.0000000
|
7
|
|
19
|
21657528
|
21657756
|
0.0000000
|
228
|
0.0000000
|
0.0000001
|
4
|
|
16
|
30572738
|
30573013
|
0.0000000
|
275
|
0.0000000
|
0.0000014
|
5
|
|
10
|
45406680
|
45406847
|
0.0000000
|
167
|
0.0000000
|
0.0000580
|
3
|
|
16
|
73100425
|
73100510
|
0.0000000
|
85
|
0.0000001
|
0.0001462
|
2
|
|
20
|
61659979
|
61660250
|
0.0000001
|
271
|
0.0000001
|
0.0000854
|
2
|
|
10
|
35484767
|
35484824
|
0.0001922
|
57
|
0.0002197
|
0.7356060
|
3
|
|
15
|
91473290
|
91473365
|
0.0005497
|
75
|
0.0005497
|
0.9445390
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mn/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mn/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mn/Mn_log2_manhattan_DMP_adj.png")

Mn, female
DMP_Mn_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Mn_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mn_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 28256
# Unadjusted, FDR<0.05: 3
# Unadjusted, pBonf<0.05: 3
# Adjusted, N = 158
# Adjusted, p<0.05: 39254
# Adjusted, FDR<0.05: 3
# Adjusted, pBonf<0.05: 2
# Adjusted, lambda: 1.350311
# Number of DMRs identified: 3
# rm(DMP_Mn_F); gc()
FDR-significant DMPs
|
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
cg11063328
|
-0.25 (-0.33 ,-0.17)
|
-6.00
|
0e+00
|
0.0008720
|
0.0009
|
chr11
|
18343203
|
GTF2H1;HPS5;HPS5;HPS5;GTF2H1
|
|
cg19425870
|
-0.24 (-0.31 ,-0.16)
|
-6.45
|
0e+00
|
0.0011946
|
0.0024
|
chr11
|
3876808
|
STIM1
|
|
cg22396353
|
-0.15 (-0.2 ,-0.09)
|
-6.10
|
2e-07
|
0.0207498
|
0.0622
|
chr22
|
46692687
|
GTSE1;GTSE1;CN5H6.4
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
16
|
73100425
|
73100510
|
0.0e+00
|
85
|
1.0e-07
|
0.0001673
|
2
|
|
6
|
3849410
|
3849690
|
5.0e-07
|
280
|
7.0e-07
|
0.0006411
|
10
|
|
11
|
76839190
|
76839217
|
4.6e-06
|
27
|
4.6e-06
|
0.0654209
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mn_F/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mn_F/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mn_F/Mn_log2_manhattan_DMP_adj.png")

Mn, male
DMP_Mn_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Mn_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mn_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 14905
# Unadjusted, FDR<0.05: 27
# Unadjusted, pBonf<0.05: 9
# Adjusted, N = 175
# Adjusted, p<0.05: 19332
# Adjusted, FDR<0.05: 32
# Adjusted, pBonf<0.05: 15
# Adjusted, lambda: 0.9962195
# Number of DMRs identified: 12
rm(DMP_Mn_M); gc()
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mn_M/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mn_M/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Mn_M/Mn_log2_manhattan_DMP_adj.png")

FDR-significant DMPs
|
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
cg03425412
|
-0.23 (-0.31 ,-0.14)
|
-5.94
|
7.0e-07
|
0.0133241
|
0.2798
|
chr20
|
21500337
|
|
|
cg04143120
|
0.42 (0.28 ,0.55)
|
6.79
|
0.0e+00
|
0.0007642
|
0.0053
|
chr11
|
72968848
|
|
|
cg04885068
|
0.19 (0.12 ,0.26)
|
6.47
|
1.0e-07
|
0.0024926
|
0.0306
|
chr1
|
9099298
|
SLC2A5;SLC2A5
|
|
cg05041382
|
-0.12 (-0.17 ,-0.07)
|
-6.39
|
2.0e-06
|
0.0288229
|
0.7782
|
chr13
|
50366546
|
KPNA3
|
|
cg05249026
|
-0.17 (-0.23 ,-0.11)
|
-2.36
|
2.0e-07
|
0.0045702
|
0.0777
|
chr16
|
11031524
|
DEXI
|
|
cg06051716
|
0.35 (0.24 ,0.46)
|
6.49
|
0.0e+00
|
0.0003949
|
0.0024
|
chr6
|
169225783
|
|
|
cg06184647
|
-0.14 (-0.2 ,-0.08)
|
-5.92
|
3.7e-06
|
0.0455095
|
1.0000
|
chr16
|
88450241
|
|
|
cg06756211
|
-0.2 (-0.27 ,-0.14)
|
-6.05
|
0.0e+00
|
0.0003949
|
0.0021
|
chr1
|
223936799
|
CAPN2;CAPN2
|
|
cg06883949
|
-0.12 (-0.17 ,-0.08)
|
-6.47
|
6.0e-07
|
0.0122154
|
0.2443
|
chr4
|
1795240
|
FGFR3;FGFR3;FGFR3
|
|
cg08072480
|
-0.14 (-0.19 ,-0.08)
|
-6.61
|
1.8e-06
|
0.0279544
|
0.7217
|
chr11
|
65292666
|
SCYL1;SCYL1
|
|
cg10088075
|
-0.11 (-0.16 ,-0.07)
|
-6.21
|
3.3e-06
|
0.0417784
|
1.0000
|
chr16
|
30407103
|
ZNF48;ZNF48
|
|
cg11480534
|
0.4 (0.24 ,0.55)
|
5.84
|
9.0e-07
|
0.0162120
|
0.3567
|
chr11
|
62255850
|
AHNAK
|
|
cg11521780
|
-0.14 (-0.18 ,-0.09)
|
-5.77
|
0.0e+00
|
0.0014335
|
0.0115
|
chr12
|
53693949
|
C12orf10
|
|
cg11755803
|
0.41 (0.25 ,0.57)
|
5.79
|
1.4e-06
|
0.0237384
|
0.5460
|
chr12
|
129000542
|
TMEM132C
|
|
cg12700904
|
-0.11 (-0.15 ,-0.06)
|
-5.94
|
1.8e-06
|
0.0279544
|
0.7268
|
chr3
|
13590720
|
FBLN2;FBLN2
|
|
cg12828656
|
-0.15 (-0.2 ,-0.11)
|
-0.50
|
0.0e+00
|
0.0001814
|
0.0007
|
chr5
|
132577108
|
FSTL4
|
|
cg13834844
|
-0.15 (-0.22 ,-0.09)
|
-5.13
|
1.8e-06
|
0.0279544
|
0.6946
|
chr10
|
102415320
|
|
|
cg13848566
|
-0.17 (-0.23 ,-0.11)
|
-6.36
|
2.0e-07
|
0.0037872
|
0.0606
|
chr9
|
89561175
|
GAS1
|
|
cg14139125
|
-0.11 (-0.15 ,-0.06)
|
-5.83
|
3.2e-06
|
0.0417784
|
1.0000
|
chr6
|
170893945
|
PDCD2;PDCD2
|
|
cg14149680
|
-0.29 (-0.38 ,-0.2)
|
-6.35
|
0.0e+00
|
0.0001169
|
0.0004
|
chr11
|
2187632
|
TH;TH;TH
|
|
cg16560774
|
-0.17 (-0.23 ,-0.11)
|
-6.46
|
0.0e+00
|
0.0017155
|
0.0154
|
chr17
|
79373381
|
BAHCC1
|
|
cg19407717
|
0.49 (0.35 ,0.64)
|
4.03
|
0.0e+00
|
0.0000387
|
0.0001
|
chr2
|
1544120
|
TPO;TPO;TPO;TPO
|
|
cg19511862
|
-0.1 (-0.14 ,-0.07)
|
-6.26
|
4.0e-07
|
0.0094291
|
0.1697
|
chr12
|
125478458
|
BRI3BP
|
|
cg19641404
|
-0.11 (-0.16 ,-0.07)
|
-5.87
|
2.4e-06
|
0.0340684
|
0.9539
|
chr2
|
232826272
|
DIS3L2
|
|
cg20414082
|
0.26 (0.16 ,0.36)
|
3.20
|
5.0e-07
|
0.0103493
|
0.1966
|
chr1
|
203002593
|
|
|
cg20504533
|
-0.22 (-0.28 ,-0.16)
|
-5.85
|
0.0e+00
|
0.0000387
|
0.0001
|
chr17
|
15848253
|
ADORA2B;ADORA2B
|
|
cg22563312
|
-0.17 (-0.23 ,-0.11)
|
-6.27
|
1.0e-07
|
0.0027236
|
0.0381
|
chr5
|
179334739
|
TBC1D9B;TBC1D9B
|
|
cg22702772
|
-0.15 (-0.2 ,-0.1)
|
-6.69
|
1.0e-07
|
0.0024926
|
0.0308
|
chr3
|
48699012
|
CELSR3
|
|
cg24196240
|
0.42 (0.27 ,0.57)
|
5.27
|
1.0e-07
|
0.0031208
|
0.0468
|
chr21
|
36096009
|
NCRNA00160
|
|
cg24948962
|
-0.22 (-0.29 ,-0.14)
|
-5.44
|
1.0e-07
|
0.0020477
|
0.0205
|
chr18
|
2906032
|
EMILIN2
|
|
cg25152909
|
0.44 (0.28 ,0.59)
|
6.08
|
1.0e-07
|
0.0024926
|
0.0324
|
chr5
|
172566090
|
C5orf41
|
|
cg25466588
|
-0.09 (-0.13 ,-0.06)
|
-5.90
|
2.8e-06
|
0.0375151
|
1.0000
|
chr3
|
23958904
|
NKIRAS1;RPL15
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
1
|
161008461
|
161008977
|
0.00e+00
|
516
|
0.00e+00
|
0.0000000
|
8
|
|
19
|
21657528
|
21658001
|
0.00e+00
|
473
|
0.00e+00
|
0.0000000
|
5
|
|
19
|
10736005
|
10736117
|
0.00e+00
|
112
|
0.00e+00
|
0.0000052
|
5
|
|
20
|
5485244
|
5485511
|
0.00e+00
|
267
|
0.00e+00
|
0.0000026
|
6
|
|
4
|
79971176
|
79971432
|
0.00e+00
|
256
|
0.00e+00
|
0.0000055
|
4
|
|
20
|
35169593
|
35169886
|
0.00e+00
|
293
|
0.00e+00
|
0.0000054
|
5
|
|
1
|
9099280
|
9099462
|
1.00e-07
|
182
|
1.00e-07
|
0.0001508
|
3
|
|
10
|
45406680
|
45406847
|
1.00e-07
|
167
|
2.00e-07
|
0.0003012
|
3
|
|
3
|
39543966
|
39544192
|
2.90e-06
|
226
|
3.90e-06
|
0.0050930
|
2
|
|
15
|
91473090
|
91473365
|
7.70e-06
|
275
|
8.70e-06
|
0.0110277
|
4
|
|
19
|
12444612
|
12444741
|
8.00e-06
|
129
|
8.70e-06
|
0.0240202
|
5
|
|
5
|
70883064
|
70883087
|
2.07e-05
|
23
|
2.07e-05
|
0.2984923
|
3
|
Pb
DMP_Pb = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Pb_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Pb')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 13157
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 17915
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9851719
# Number of DMRs identified: 8
# rm(DMP_Pb); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
10
|
135051021
|
135051581
|
0e+00
|
560
|
0e+00
|
0.0000000
|
11
|
|
22
|
45704901
|
45705265
|
0e+00
|
364
|
0e+00
|
0.0000000
|
7
|
|
3
|
130745441
|
130745685
|
0e+00
|
244
|
1e-07
|
0.0000532
|
10
|
|
22
|
19746155
|
19746368
|
1e-07
|
213
|
1e-07
|
0.0000952
|
3
|
|
14
|
104690039
|
104690244
|
1e-07
|
205
|
1e-07
|
0.0001426
|
5
|
|
5
|
23507449
|
23507656
|
1e-07
|
207
|
1e-07
|
0.0001951
|
5
|
|
7
|
155283139
|
155283424
|
1e-07
|
285
|
1e-07
|
0.0001464
|
3
|
|
6
|
2891972
|
2892152
|
1e-07
|
180
|
1e-07
|
0.0002542
|
5
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Pb/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Pb/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Pb/Pb_log2_manhattan_DMP_adj.png")

Pb, female
DMP_Pb_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Pb_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Pb_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 10571
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 12173
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.7458629
# Number of identified DMR: 0
# rm(DMP_Pb_F); gc()
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Pb_F/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Pb_F/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Pb_F/Pb_log2_manhattan_DMP_adj.png")

Pb, male
DMP_Pb_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Pb_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Pb_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 18362
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 12544
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8738391
# Number of DMRs identified: 6
# rm(DMP_Pb_M); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
6
|
33084548
|
33084985
|
0.0000000
|
437
|
0.0000000
|
0.0000000
|
12
|
|
1
|
68512649
|
68513063
|
0.0000000
|
414
|
0.0000000
|
0.0000008
|
7
|
|
6
|
31148331
|
31148748
|
0.0000000
|
417
|
0.0000000
|
0.0000009
|
14
|
|
22
|
45704987
|
45705265
|
0.0000000
|
278
|
0.0000001
|
0.0000607
|
5
|
|
22
|
19751653
|
19751899
|
0.0000001
|
246
|
0.0000001
|
0.0001654
|
3
|
|
19
|
55973098
|
55973234
|
0.0002477
|
136
|
0.0002477
|
0.5125157
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Pb_M/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Pb_M/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Pb_M/Pb_log2_manhattan_DMP_adj.png")

Se
DMP_Se = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Se_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Se')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 17270
# Unadjusted, FDR<0.05: 1
# Unadjusted, pBonf<0.05: 1
# Adjusted, N = 333
# Adjusted, p<0.05: 19895
# Adjusted, FDR<0.05: 4
# Adjusted, pBonf<0.05: 2
# Adjusted, lambda: 0.9687492
# Number of DMRs identified: 3
# rm(DMP_Se); gc()
FDR-significant DMPs
|
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
cg08760128
|
0.21 (0.13 ,0.28)
|
6.73
|
2e-07
|
0.0327152
|
0.0981
|
chr16
|
4723507
|
MGRN1;MGRN1;MGRN1;MGRN1
|
|
cg10145926
|
0.55 (0.35 ,0.75)
|
5.31
|
1e-07
|
0.0203812
|
0.0408
|
chr14
|
95875792
|
C14orf139
|
|
cg13434714
|
-0.42 (-0.56 ,-0.28)
|
-5.77
|
0e+00
|
0.0070511
|
0.0071
|
chr12
|
6936787
|
LEPREL2
|
|
cg26708724
|
0.59 (0.36 ,0.81)
|
6.73
|
5e-07
|
0.0491345
|
0.1965
|
chr4
|
187509785
|
FAT1
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
19
|
50194119
|
50194252
|
0
|
133
|
0
|
1.26e-05
|
5
|
|
17
|
47091977
|
47092178
|
0
|
201
|
0
|
9.00e-06
|
4
|
|
6
|
49681177
|
49681391
|
0
|
214
|
0
|
6.89e-05
|
7
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Se/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Se/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Se/Se_log2_manhattan_DMP_adj.png")

Se, female
DMP_Se_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Se_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Se_F')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 26254
# Unadjusted, FDR<0.05: 9
# Unadjusted, pBonf<0.05: 2
# Adjusted, N = 158
# Adjusted, p<0.05: 15227
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9131987
# Number of DMRs identified: 5
# rm(DMP_Se_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
10
|
38146245
|
38146671
|
0.0e+00
|
426
|
0.0e+00
|
0.0000001
|
9
|
|
6
|
49681177
|
49681391
|
0.0e+00
|
214
|
0.0e+00
|
0.0000003
|
7
|
|
10
|
38299241
|
38299574
|
0.0e+00
|
333
|
0.0e+00
|
0.0000053
|
9
|
|
1
|
236686563
|
236686804
|
0.0e+00
|
241
|
0.0e+00
|
0.0000613
|
4
|
|
6
|
42928055
|
42928200
|
7.9e-06
|
145
|
7.9e-06
|
0.0213843
|
5
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Se_F/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Se_F/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Se_F/Se_log2_manhattan_DMP_adj.png")

Se, male
DMP_Se_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Se_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Se_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 15593
# Unadjusted, FDR<0.05: 42
# Unadjusted, pBonf<0.05: 12
# Adjusted, N = 175
# Adjusted, p<0.05: 14283
# Adjusted, FDR<0.05: 28
# Adjusted, pBonf<0.05: 7
# Adjusted, lambda: 0.8126609
# Number of DMRs identified: 3
# rm(DMP_Se_M); gc()
FDR-significant DMPs
|
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
cg00908120
|
0.6 (0.37 ,0.83)
|
6.29
|
1.1e-06
|
0.0298488
|
0.4477
|
chr16
|
72872925
|
ZFHX3;ZFHX3
|
|
cg01007589
|
0.79 (0.49 ,1.1)
|
4.79
|
7.0e-07
|
0.0210168
|
0.2732
|
chr19
|
49894178
|
CCDC155
|
|
cg01588060
|
-0.28 (-0.39 ,-0.18)
|
-5.90
|
5.0e-07
|
0.0172784
|
0.1867
|
chr6
|
2245749
|
GMDS;GMDS
|
|
cg04692924
|
-0.6 (-0.81 ,-0.39)
|
-6.58
|
1.0e-07
|
0.0053838
|
0.0323
|
chr1
|
161720042
|
DUSP12
|
|
cg05051957
|
-0.66 (-0.87 ,-0.44)
|
-5.61
|
0.0e+00
|
0.0009331
|
0.0037
|
chr8
|
141522459
|
CHRAC1;CHRAC1
|
|
cg06723863
|
-0.35 (-0.47 ,-0.22)
|
-5.99
|
1.0e-07
|
0.0055617
|
0.0389
|
chr16
|
68270129
|
ESRP2;ESRP2
|
|
cg07380021
|
-0.51 (-0.72 ,-0.3)
|
-5.43
|
3.0e-06
|
0.0474750
|
1.0000
|
chr1
|
206755252
|
RASSF5;RASSF5;RASSF5
|
|
cg07599133
|
-0.34 (-0.47 ,-0.2)
|
-5.96
|
1.8e-06
|
0.0428804
|
0.7290
|
chr19
|
35068628
|
LOC643719
|
|
cg08459368
|
0.52 (0.31 ,0.73)
|
2.70
|
2.7e-06
|
0.0474750
|
1.0000
|
chr11
|
61974948
|
SCGB2A1
|
|
cg08760128
|
0.28 (0.17 ,0.39)
|
6.73
|
1.8e-06
|
0.0428804
|
0.7131
|
chr16
|
4723507
|
MGRN1;MGRN1;MGRN1;MGRN1
|
|
cg10266648
|
0.84 (0.5 ,1.19)
|
5.98
|
3.0e-06
|
0.0474750
|
1.0000
|
chr2
|
106560529
|
|
|
cg11443888
|
0.28 (0.17 ,0.39)
|
2.36
|
2.3e-06
|
0.0434950
|
0.9134
|
chr6
|
44244590
|
TMEM151B
|
|
cg11608893
|
0.85 (0.56 ,1.14)
|
6.08
|
0.0e+00
|
0.0022825
|
0.0114
|
chr6
|
32059542
|
TNXB
|
|
cg12243007
|
0.44 (0.27 ,0.61)
|
-0.77
|
1.1e-06
|
0.0298488
|
0.4290
|
chr17
|
184018
|
RPH3AL
|
|
cg12897502
|
-0.83 (-1.15 ,-0.52)
|
6.10
|
6.0e-07
|
0.0193412
|
0.2321
|
chr8
|
67425316
|
C8orf46
|
|
cg13434714
|
-0.63 (-0.8 ,-0.45)
|
-5.78
|
0.0e+00
|
0.0000222
|
0.0000
|
chr12
|
6936787
|
LEPREL2
|
|
cg16656826
|
0.29 (0.17 ,0.4)
|
0.14
|
2.2e-06
|
0.0434950
|
0.8735
|
chr5
|
159343871
|
ADRA1B;ADRA1B
|
|
cg17515932
|
0.79 (0.47 ,1.12)
|
4.46
|
3.2e-06
|
0.0474750
|
1.0000
|
chr7
|
156190074
|
|
|
cg18377660
|
0.69 (0.43 ,0.95)
|
5.65
|
5.0e-07
|
0.0172784
|
0.1901
|
chr1
|
57535755
|
DAB1
|
|
cg19005275
|
0.59 (0.38 ,0.81)
|
4.29
|
3.0e-07
|
0.0111028
|
0.0999
|
chr12
|
113588263
|
CCDC42B
|
|
cg21373263
|
0.84 (0.57 ,1.11)
|
3.29
|
0.0e+00
|
0.0009331
|
0.0031
|
chr10
|
126751982
|
CTBP2;CTBP2
|
|
cg21864868
|
0.58 (0.34 ,0.81)
|
4.22
|
3.4e-06
|
0.0474955
|
1.0000
|
chr17
|
46673002
|
LOC404266;LOC404266;LOC404266;LOC404266;LOC404266
|
|
cg22286640
|
-0.73 (-1.03 ,-0.44)
|
-4.65
|
2.2e-06
|
0.0434950
|
0.8497
|
chr8
|
67026828
|
|
|
cg23994888
|
-0.52 (-0.73 ,-0.31)
|
-5.91
|
2.3e-06
|
0.0434950
|
0.9045
|
chr1
|
6052642
|
NPHP4
|
|
cg25067702
|
-0.63 (-0.86 ,-0.4)
|
-6.40
|
2.0e-07
|
0.0079009
|
0.0632
|
chr17
|
70723227
|
SLC39A11;SLC39A11
|
|
cg25469351
|
1.29 (0.76 ,1.82)
|
5.96
|
3.1e-06
|
0.0474750
|
1.0000
|
chr7
|
6191921
|
USP42
|
|
cg26342676
|
0.61 (0.36 ,0.86)
|
4.56
|
3.0e-06
|
0.0474750
|
1.0000
|
chr14
|
37639757
|
SLC25A21;SLC25A21;LOC100129794
|
|
cg26708724
|
1.01 (0.73 ,1.3)
|
6.72
|
0.0e+00
|
0.0000140
|
0.0000
|
chr4
|
187509785
|
FAT1
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
70723226
|
70723386
|
0e+00
|
160
|
0e+00
|
0.0000001
|
2
|
|
4
|
24796918
|
24797176
|
0e+00
|
258
|
0e+00
|
0.0000151
|
6
|
|
10
|
121578383
|
121578639
|
2e-07
|
256
|
2e-07
|
0.0002571
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Se_M/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Se_M/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Se_M/Se_log2_manhattan_DMP_adj.png")

Zn
DMP_Zn = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Zn_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Zn')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 12854
# Unadjusted, FDR<0.05: 1
# Unadjusted, pBonf<0.05: 1
# Adjusted, N = 333
# Adjusted, p<0.05: 23218
# Adjusted, FDR<0.05: 13
# Adjusted, pBonf<0.05: 3
# Adjusted, lambda: 1.097804
# Number of DMRs identified: 11
# rm(DMP_Zn); gc()
FDR-significant DMPs
|
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
cg00082497
|
-0.28 (-0.38 ,-0.18)
|
-5.32
|
1.0e-07
|
0.0129186
|
0.0269
|
chr1
|
32802133
|
MARCKSL1
|
|
cg00908120
|
0.49 (0.3 ,0.67)
|
6.26
|
4.0e-07
|
0.0197441
|
0.1382
|
chr16
|
72872925
|
ZFHX3;ZFHX3
|
|
cg04015129
|
0.65 (0.4 ,0.91)
|
4.28
|
8.0e-07
|
0.0273868
|
0.3108
|
chr10
|
1058036
|
GTPBP4
|
|
cg05573434
|
0.42 (0.26 ,0.57)
|
-3.15
|
3.0e-07
|
0.0175293
|
0.1052
|
chr4
|
7648540
|
SORCS2
|
|
cg06723863
|
-0.25 (-0.35 ,-0.15)
|
-5.98
|
1.6e-06
|
0.0476390
|
0.6193
|
chr16
|
68270129
|
ESRP2;ESRP2
|
|
cg08459368
|
0.59 (0.38 ,0.81)
|
2.65
|
1.0e-07
|
0.0129186
|
0.0388
|
chr11
|
61974948
|
SCGB2A1
|
|
cg10653573
|
0.82 (0.5 ,1.13)
|
5.43
|
8.0e-07
|
0.0273868
|
0.3279
|
chr8
|
141347297
|
TRAPPC9;TRAPPC9
|
|
cg13434714
|
-0.49 (-0.64 ,-0.33)
|
-5.77
|
0.0e+00
|
0.0012795
|
0.0013
|
chr12
|
6936787
|
LEPREL2
|
|
cg15528091
|
-0.31 (-0.43 ,-0.19)
|
-6.36
|
7.0e-07
|
0.0273868
|
0.2933
|
chr19
|
18119069
|
ARRDC2;ARRDC2;ARRDC2
|
|
cg16496814
|
0.21 (0.13 ,0.3)
|
5.21
|
6.0e-07
|
0.0273868
|
0.2425
|
chr11
|
9778721
|
|
|
cg19011752
|
0.25 (0.15 ,0.34)
|
-2.54
|
8.0e-07
|
0.0273868
|
0.3286
|
chr21
|
45772638
|
TRPM2
|
|
cg23477849
|
0.26 (0.16 ,0.35)
|
4.88
|
2.0e-07
|
0.0156531
|
0.0783
|
chr19
|
5698492
|
LONP1
|
|
cg25954729
|
-0.21 (-0.29 ,-0.14)
|
-6.34
|
2.0e-07
|
0.0156531
|
0.0704
|
chr11
|
66610784
|
RCE1;C11orf80;RCE1
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
12
|
54070516
|
54070610
|
0.0000000
|
94
|
0.0000000
|
0.0000047
|
5
|
|
19
|
18118799
|
18119069
|
0.0000000
|
270
|
0.0000000
|
0.0000090
|
3
|
|
10
|
124638975
|
124639260
|
0.0000000
|
285
|
0.0000001
|
0.0000227
|
12
|
|
4
|
7648539
|
7648627
|
0.0000001
|
88
|
0.0000002
|
0.0002692
|
2
|
|
6
|
41168800
|
41169049
|
0.0000001
|
249
|
0.0000002
|
0.0001710
|
6
|
|
17
|
79503641
|
79503877
|
0.0000001
|
236
|
0.0000002
|
0.0002055
|
4
|
|
8
|
41655672
|
41655894
|
0.0000001
|
222
|
0.0000002
|
0.0002427
|
4
|
|
6
|
32064145
|
32064258
|
0.0000002
|
113
|
0.0000003
|
0.0007474
|
10
|
|
22
|
45704987
|
45705042
|
0.0000002
|
55
|
0.0000003
|
0.0016449
|
4
|
|
20
|
25129506
|
25129562
|
0.0000021
|
56
|
0.0000023
|
0.0149234
|
5
|
|
20
|
35169593
|
35169609
|
0.0095658
|
16
|
0.0095658
|
1.0000000
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Zn/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Zn/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Zn/Zn_log2_manhattan_DMP_adj.png")

Zn, female
DMP_Zn_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Zn_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Zn_F')
# # Unadjusted, N = 158
# Unadjusted, p<0.05: 12830
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 17143
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9412223
# Number of DMRs identified: 3
# rm(DMP_Zn_F); gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
11
|
73357018
|
73357396
|
0.0e+00
|
378
|
0.0e+00
|
0.0000000
|
8
|
|
1
|
120174148
|
120174361
|
9.0e-07
|
213
|
1.4e-06
|
0.0017026
|
2
|
|
10
|
124638975
|
124639012
|
3.2e-06
|
37
|
3.2e-06
|
0.0336353
|
4
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Zn_F/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Zn_F/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Zn_F/Zn_log2_manhattan_DMP_adj.png")

Zn, male
DMP_Zn_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Zn_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Zn_M')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 16787
# Unadjusted, FDR<0.05: 36
# Unadjusted, pBonf<0.05: 8
# Adjusted, N = 175
# Adjusted, p<0.05: 14737
# Adjusted, FDR<0.05: 36
# Adjusted, pBonf<0.05: 3
# Adjusted, lambda: 0.8766913
# Number of DMRs identified: 16
# rm(DMP_Zn_M); gc()
FDR-significant DMPs
|
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
cg00908120
|
0.8 (0.52 ,1.07)
|
6.29
|
0.0e+00
|
0.0063443
|
0.0165
|
chr16
|
72872925
|
ZFHX3;ZFHX3
|
|
cg01007589
|
0.91 (0.55 ,1.27)
|
4.79
|
2.0e-06
|
0.0314161
|
0.8041
|
chr19
|
49894178
|
CCDC155
|
|
cg01447660
|
0.42 (0.25 ,0.59)
|
-0.92
|
3.7e-06
|
0.0417381
|
1.0000
|
chr2
|
69152678
|
|
|
cg02196294
|
-0.29 (-0.41 ,-0.17)
|
-5.41
|
3.6e-06
|
0.0414185
|
1.0000
|
chr6
|
39197260
|
KCNK5
|
|
cg02490920
|
0.39 (0.24 ,0.55)
|
1.34
|
1.2e-06
|
0.0201387
|
0.4632
|
chr3
|
50304406
|
SEMA3B;SEMA3B
|
|
cg02711608
|
0.54 (0.35 ,0.74)
|
-2.09
|
2.0e-07
|
0.0120512
|
0.0878
|
chr19
|
47287964
|
SLC1A5;SLC1A5;SLC1A5;SLC1A5
|
|
cg02968175
|
0.33 (0.2 ,0.46)
|
5.76
|
7.0e-07
|
0.0154847
|
0.2851
|
chr16
|
4690020
|
MGRN1;MGRN1;MGRN1;MGRN1
|
|
cg03352332
|
0.9 (0.57 ,1.24)
|
5.54
|
2.0e-07
|
0.0120512
|
0.0964
|
chr3
|
186360953
|
FETUB
|
|
cg04015129
|
0.86 (0.55 ,1.18)
|
4.27
|
2.0e-07
|
0.0120512
|
0.0877
|
chr10
|
1058036
|
GTPBP4
|
|
cg04374006
|
0.26 (0.16 ,0.37)
|
-0.27
|
2.9e-06
|
0.0377171
|
1.0000
|
chr19
|
33556395
|
RHPN2
|
|
cg04406071
|
-0.32 (-0.45 ,-0.2)
|
-6.07
|
7.0e-07
|
0.0154847
|
0.2898
|
chr17
|
59489784
|
C17orf82
|
|
cg04692924
|
-0.66 (-0.92 ,-0.41)
|
-6.58
|
7.0e-07
|
0.0154847
|
0.2942
|
chr1
|
161720042
|
DUSP12
|
|
cg05051957
|
-0.66 (-0.92 ,-0.39)
|
-5.61
|
2.3e-06
|
0.0319338
|
0.8941
|
chr8
|
141522459
|
CHRAC1;CHRAC1
|
|
cg06723863
|
-0.36 (-0.51 ,-0.22)
|
-5.99
|
3.2e-06
|
0.0406663
|
1.0000
|
chr16
|
68270129
|
ESRP2;ESRP2
|
|
cg07380021
|
-0.65 (-0.9 ,-0.41)
|
-5.43
|
5.0e-07
|
0.0134172
|
0.2147
|
chr1
|
206755252
|
RASSF5;RASSF5;RASSF5
|
|
cg08760128
|
0.36 (0.23 ,0.49)
|
6.73
|
2.0e-07
|
0.0120512
|
0.0686
|
chr16
|
4723507
|
MGRN1;MGRN1;MGRN1;MGRN1
|
|
cg10266648
|
1.04 (0.64 ,1.45)
|
5.98
|
1.2e-06
|
0.0201387
|
0.4573
|
chr2
|
106560529
|
|
|
cg10653573
|
1.42 (0.91 ,1.93)
|
5.37
|
2.0e-07
|
0.0120512
|
0.0662
|
chr8
|
141347297
|
TRAPPC9;TRAPPC9
|
|
cg10923018
|
0.31 (0.18 ,0.44)
|
2.73
|
3.5e-06
|
0.0414185
|
1.0000
|
chr6
|
31743769
|
C6orf27
|
|
cg11761483
|
-0.72 (-0.99 ,-0.45)
|
-5.60
|
5.0e-07
|
0.0134172
|
0.1942
|
chr17
|
70723386
|
SLC39A11;SLC39A11
|
|
cg13434714
|
-0.84 (-1.04 ,-0.63)
|
-5.78
|
0.0e+00
|
0.0000001
|
0.0000
|
chr12
|
6936787
|
LEPREL2
|
|
cg14230280
|
1.22 (0.73 ,1.71)
|
4.28
|
2.2e-06
|
0.0314161
|
0.8482
|
chr9
|
132502800
|
PTGES
|
|
cg16496814
|
0.32 (0.2 ,0.44)
|
5.22
|
4.0e-07
|
0.0134172
|
0.1415
|
chr11
|
9778721
|
|
|
cg16656826
|
0.34 (0.21 ,0.48)
|
0.14
|
2.1e-06
|
0.0314161
|
0.8405
|
chr5
|
159343871
|
ADRA1B;ADRA1B
|
|
cg17155018
|
-1.02 (-1.44 ,-0.6)
|
1.39
|
4.3e-06
|
0.0469139
|
1.0000
|
chr6
|
111953066
|
|
|
cg18037826
|
0.41 (0.25 ,0.57)
|
4.29
|
1.1e-06
|
0.0201387
|
0.4346
|
chr12
|
109273835
|
DAO
|
|
cg19005275
|
0.75 (0.49 ,1)
|
4.29
|
0.0e+00
|
0.0063443
|
0.0190
|
chr12
|
113588263
|
CCDC42B
|
|
cg19532212
|
0.76 (0.47 ,1.05)
|
4.42
|
5.0e-07
|
0.0134172
|
0.2072
|
chr17
|
56769430
|
TEX14;RAD51C;TEX14;RAD51C
|
|
cg21373263
|
0.88 (0.55 ,1.21)
|
3.29
|
5.0e-07
|
0.0134172
|
0.2067
|
chr10
|
126751982
|
CTBP2;CTBP2
|
|
cg22240394
|
1.22 (0.77 ,1.68)
|
6.82
|
4.0e-07
|
0.0134172
|
0.1707
|
chr3
|
186211630
|
|
|
cg22413938
|
-0.39 (-0.54 ,-0.23)
|
-4.56
|
3.3e-06
|
0.0406663
|
1.0000
|
chr14
|
78447481
|
|
|
cg23477849
|
0.38 (0.23 ,0.53)
|
4.90
|
1.8e-06
|
0.0292663
|
0.7024
|
chr19
|
5698492
|
LONP1
|
|
cg23601521
|
0.8 (0.5 ,1.1)
|
4.87
|
5.0e-07
|
0.0134172
|
0.2111
|
chr2
|
50275179
|
NRXN1;NRXN1;NRXN1
|
|
cg25954729
|
-0.3 (-0.42 ,-0.19)
|
-6.37
|
4.0e-07
|
0.0134172
|
0.1746
|
chr11
|
66610784
|
RCE1;C11orf80;RCE1
|
|
cg26608798
|
0.39 (0.23 ,0.56)
|
0.58
|
2.8e-06
|
0.0377171
|
1.0000
|
chr16
|
33853544
|
|
|
cg26708724
|
0.92 (0.56 ,1.28)
|
6.72
|
1.0e-06
|
0.0198743
|
0.3975
|
chr4
|
187509785
|
FAT1
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
70723226
|
70723386
|
0.0000000
|
160
|
0.0000000
|
0.0000021
|
2
|
|
10
|
121578136
|
121578639
|
0.0000000
|
503
|
0.0000000
|
0.0000011
|
4
|
|
14
|
78447480
|
78447640
|
0.0000000
|
160
|
0.0000000
|
0.0000148
|
3
|
|
19
|
50194119
|
50194252
|
0.0000000
|
133
|
0.0000000
|
0.0000199
|
5
|
|
4
|
24796918
|
24797176
|
0.0000000
|
258
|
0.0000000
|
0.0000115
|
6
|
|
4
|
186732836
|
186733060
|
0.0000000
|
224
|
0.0000000
|
0.0000157
|
7
|
|
14
|
76734326
|
76734605
|
0.0000000
|
279
|
0.0000000
|
0.0000225
|
5
|
|
21
|
45773781
|
45773997
|
0.0000000
|
216
|
0.0000000
|
0.0000319
|
2
|
|
5
|
135416204
|
135416613
|
0.0000000
|
409
|
0.0000000
|
0.0000219
|
9
|
|
11
|
63679431
|
63679637
|
0.0000001
|
206
|
0.0000002
|
0.0001797
|
2
|
|
20
|
62716331
|
62716606
|
0.0000001
|
275
|
0.0000002
|
0.0001584
|
4
|
|
17
|
78549323
|
78549371
|
0.0000001
|
48
|
0.0000002
|
0.0011866
|
3
|
|
5
|
1868136
|
1868357
|
0.0000003
|
221
|
0.0000004
|
0.0005635
|
4
|
|
22
|
45704987
|
45705042
|
0.0000017
|
55
|
0.0000019
|
0.0120479
|
4
|
|
5
|
176755392
|
176755449
|
0.0000125
|
57
|
0.0000133
|
0.0826896
|
2
|
|
2
|
88583556
|
88583805
|
0.0001149
|
249
|
0.0001149
|
0.1664579
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Zn_M/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Zn_M/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7/Zn_M/Zn_log2_manhattan_DMP_adj.png")
